{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T23:59:51Z","timestamp":1771027191238,"version":"3.50.1"},"reference-count":82,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2024,8,25]],"date-time":"2024-08-25T00:00:00Z","timestamp":1724544000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170432"],"award-info":[{"award-number":["32170432"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31401961"],"award-info":[{"award-number":["31401961"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["2021XBZG_XBQNXZ_A_005"],"award-info":[{"award-number":["2021XBZG_XBQNXZ_A_005"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["18YYJC0171"],"award-info":[{"award-number":["18YYJC0171"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Western Lights Young Scholars Plan of Chinese Academy of Sciences","award":["32170432"],"award-info":[{"award-number":["32170432"]}]},{"name":"Western Lights Young Scholars Plan of Chinese Academy of Sciences","award":["31401961"],"award-info":[{"award-number":["31401961"]}]},{"name":"Western Lights Young Scholars Plan of Chinese Academy of Sciences","award":["2021XBZG_XBQNXZ_A_005"],"award-info":[{"award-number":["2021XBZG_XBQNXZ_A_005"]}]},{"name":"Western Lights Young Scholars Plan of Chinese Academy of Sciences","award":["18YYJC0171"],"award-info":[{"award-number":["18YYJC0171"]}]},{"name":"Sichuan Science and Technology Program","award":["32170432"],"award-info":[{"award-number":["32170432"]}]},{"name":"Sichuan Science and Technology Program","award":["31401961"],"award-info":[{"award-number":["31401961"]}]},{"name":"Sichuan Science and Technology Program","award":["2021XBZG_XBQNXZ_A_005"],"award-info":[{"award-number":["2021XBZG_XBQNXZ_A_005"]}]},{"name":"Sichuan Science and Technology Program","award":["18YYJC0171"],"award-info":[{"award-number":["18YYJC0171"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Newts are excellent vertebrate models for investigating tissue regeneration due to their remarkable regenerative capabilities. To investigate the mRNA and microRNAs (miRNAs) profiles within the blastema niche of regenerating newt limbs, we amputated the limbs of Chinese fire belly newts (Cynops orientalis) and conducted comprehensive analyses of the transcriptome and microRNA profiles at five distinct time points post-amputation (0 hours, 1 day, 5 days 10 days and 20 days). We identified 24 significantly differentially expressed (DE) genes and 20 significantly DE miRNAs. Utilizing weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) enrichment analysis, we identified four genes likely to playing crucial roles in the early stages of limb regeneration: Cemip, Rhou, Gpd2 and Pcna. Moreover, mRNA\u2013miRNA integration analysis uncovered seven human miRNAs (miR-19b-1, miR-19b-2, miR-21-5p, miR-127-5p, miR-150-5p, miR-194-5p, and miR-210-5p) may regulate the expression of these four key genes. The temporal expression patterns of these key genes and miRNAs further validated the robustness of the identified mRNA-miRNA landscape. Our study successfully identified candidate key genes and elucidated a portion of the genetic regulatory mechanisms involved in newt limb regeneration. These findings offer valuable insights for further exploration of the intricate processes of tissue regeneration.<\/jats:p>","DOI":"10.3390\/ijms25179225","type":"journal-article","created":{"date-parts":[[2024,8,26]],"date-time":"2024-08-26T07:53:37Z","timestamp":1724658817000},"page":"9225","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["The mRNA and microRNA Landscape of the Blastema Niche in Regenerating Newt Limbs"],"prefix":"10.3390","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-1669-0117","authenticated-orcid":false,"given":"Qi","family":"Zhang","sequence":"first","affiliation":[{"name":"Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0272-3256","authenticated-orcid":false,"given":"Bin","family":"Lu","sequence":"additional","affiliation":[{"name":"Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,8,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"dev167700","DOI":"10.1242\/dev.167700","article-title":"Model systems for regeneration: Salamanders","volume":"146","author":"Joven","year":"2019","journal-title":"Development"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1002\/jcp.29920","article-title":"Exploring the role of microRNAs in axolotl regeneration","volume":"236","year":"2021","journal-title":"J. Cell. Physiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/bs.ctdb.2020.11.009","article-title":"Salamanders: The molecular basis of tissue regeneration and its relevance to human disease","volume":"145","author":"Echeverri","year":"2021","journal-title":"Curr. Top. Dev. Biol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1002\/reg2.93","article-title":"Limb regeneration in a direct-developing terrestrial salamander, Bolitoglossa ramosi (Caudata: Plethodontidae): Limb regeneration in plethodontid salamanders","volume":"4","author":"Molina","year":"2017","journal-title":"Regeneration"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1080\/19768354.2012.729537","article-title":"Endogenous retinoic acid mediates the early events in salamander limb regeneration","volume":"16","author":"Lee","year":"2012","journal-title":"Anim. Cells Syst."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-0716-2659-7_1","article-title":"Salamanders as Key Models for Development and Regeneration Research","volume":"2562","author":"Maden","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Stewart, R., Rasc\u00f3n, C.A., Tian, S., Nie, J., Barry, C., Chu, L.-F., Ardalani, H., Wagner, R.J., Probasco, M.D., and Bolin, J.M. (2013). Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema. PLoS Comput. Biol., 9.","DOI":"10.1371\/journal.pcbi.1002936"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"13364","DOI":"10.1038\/ncomms13364","article-title":"Tetrapod limb and sarcopterygian fin regeneration share a core genetic programme","volume":"7","author":"Nogueira","year":"2016","journal-title":"Nat. Commun."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1038\/nature02871","article-title":"The functions of animal microRNAs","volume":"431","author":"Ambros","year":"2004","journal-title":"Nature"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1038\/nature03702","article-title":"MicroRNA expression profiles classify human cancers","volume":"435","author":"Lu","year":"2005","journal-title":"Nature"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"10513","DOI":"10.1073\/pnas.0804549105","article-title":"Circulating microRNAs as stable blood-based markers for cancer detection","volume":"105","author":"Mitchell","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1038\/nrm3904","article-title":"Remodelling the extracellular matrix in development and disease","volume":"15","author":"Bonnans","year":"2014","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1242\/dmm.004077","article-title":"Remodeling and homeostasis of the extracellular matrix: Implications for fibrotic diseases and cancer","volume":"4","author":"Cox","year":"2011","journal-title":"Dis. Model. Mech."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1016\/j.cell.2006.10.018","article-title":"Wnt\/\u03b2-Catenin Signaling in Development and Disease","volume":"127","author":"Clevers","year":"2006","journal-title":"Cell"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13619-020-00072-2","article-title":"The interaction of Notch and Wnt signaling pathways in vertebrate regeneration","volume":"10","author":"Gao","year":"2021","journal-title":"Cell Regen."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1146\/annurev.cellbio.20.010403.113126","article-title":"THE WNT SIGNALING PATHWAY IN DEVELOPMENT AND DISEASE","volume":"20","author":"Logan","year":"2004","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.devcel.2009.06.016","article-title":"Wnt\/\u03b2-Catenin Signaling: Components, Mechanisms, and Diseases","volume":"17","author":"Macdonald","year":"2009","journal-title":"Dev. Cell"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1704","DOI":"10.1126\/science.1092053","article-title":"Cell Migration: Integrating Signals from Front to Back","volume":"302","author":"Ridley","year":"2003","journal-title":"Science"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1172\/JCI39104","article-title":"The basics of epithelial-mesenchymal transition","volume":"119","author":"Kalluri","year":"2009","journal-title":"J. Clin. Investig."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"3202","DOI":"10.2353\/ajpath.2010.100594","article-title":"Blockade of Transforming Growth Factor-\u03b21 Accelerates Lymphatic Regeneration during Wound Repair","volume":"177","author":"Avraham","year":"2010","journal-title":"Am. J. Pathol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1021\/acs.jproteome.8b00778","article-title":"Integrative Analysis of MicroRNAome, Transcriptome, and Proteome during the Limb Regeneration of Cynops orientalis","volume":"18","author":"Yu","year":"2019","journal-title":"J. Proteome Res."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"2510","DOI":"10.1111\/all.14762","article-title":"Whole genome sequencing identifies novel genetic mutations in patients with eczema herpeticum","volume":"76","author":"Bin","year":"2021","journal-title":"Allergy"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/S1016-8478(23)17561-3","article-title":"v-Crk Induces Rac-dependent Membrane Ruffling and Cell Migration in CAS-deficient Embryonic Fibroblasts","volume":"25","author":"Sung","year":"2008","journal-title":"Mol. Cells"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1177\/0363546513507766","article-title":"The Anti-inflammatory and Matrix Restorative Mechanisms of Platelet-Rich Plasma in Osteoarthritis","volume":"42","author":"Sundman","year":"2014","journal-title":"Am. J. Sports Med."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/j.acthis.2017.11.002","article-title":"Silencing of CEMIP suppresses Wnt\/\u03b2-catenin\/Snail signaling transduction and inhibits EMT program of colorectal cancer cells","volume":"120","author":"Liang","year":"2018","journal-title":"Acta Histochem."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"5612","DOI":"10.1073\/pnas.1215432110","article-title":"KIAA1199, a deafness gene of unknown function, is a new hyaluronan binding protein involved in hyaluronan depolymerization","volume":"110","author":"Yoshida","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"426","DOI":"10.2183\/pjab.86.426","article-title":"Intracellular trafficking of ceramide by ceramide transfer protein","volume":"86","author":"Hanada","year":"2010","journal-title":"Proc. Jpn. Acad. Ser. B"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1126\/science.1142883","article-title":"Monitoring of Blood Vessels and Tissues by a Population of Monocytes with Patrolling Behavior","volume":"317","author":"Auffray","year":"2007","journal-title":"Science"},{"key":"ref_29","first-page":"552","article-title":"Bases moleculares de las interacciones leucocito-endotelio durante la respuesta inflamatoria","volume":"62","author":"Barreiro","year":"2009","journal-title":"REC Interv. Cardiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1111\/boc.201800062","article-title":"The atypical RhoU\/Wrch1 Rho GTPase controls cell proliferation and apoptosis in the gut epithelium","volume":"111","author":"Slaymi","year":"2019","journal-title":"Biol. Cell"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1042\/BJ20081386","article-title":"How mitochondria produce reactive oxygen species","volume":"417","author":"Murphy","year":"2009","journal-title":"Biochem. J."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"3137","DOI":"10.1172\/JCI74593","article-title":"Hypomorphic PCNA mutation underlies a human DNA repair disorder","volume":"124","author":"Baple","year":"2014","journal-title":"J. Clin. Investig."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1038\/nature25458","article-title":"The axolotl genome and the evolution of key tissue formation regulators","volume":"554","author":"Nowoshilow","year":"2018","journal-title":"Nature"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1016\/j.celrep.2016.12.063","article-title":"A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors","volume":"18","author":"Bryant","year":"2017","journal-title":"Cell Rep."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1016\/j.stem.2013.11.007","article-title":"Fundamental Differences in Dedifferentiation and Stem Cell Recruitment during Skeletal Muscle Regeneration in Two Salamander Species","volume":"14","author":"Wang","year":"2014","journal-title":"Cell Stem Cell"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1002\/reg2.25","article-title":"Plasticity for axolotl lens regeneration is associated with age-related changes in gene expression","volume":"1","author":"Sousounis","year":"2014","journal-title":"Regeneration"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1038\/ncomms1389","article-title":"Regenerative capacity in newts is not altered by repeated regeneration and ageing","volume":"2","author":"Eguchi","year":"2011","journal-title":"Nat. Commun."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1038\/nature17889","article-title":"Limb regrowth takes two","volume":"533","author":"Torres","year":"2016","journal-title":"Nature"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1146\/annurev-cellbio-092910-154115","article-title":"Limb Regeneration: A New Development?","volume":"27","author":"Nacu","year":"2011","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1057","DOI":"10.1084\/jem.20070075","article-title":"Inflammatory monocytes recruited after skeletal muscle injury switch into antiinflammatory macrophages to support myogenesis","volume":"204","author":"Arnold","year":"2007","journal-title":"J. Exp. Med."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.phrs.2008.07.009","article-title":"Immune cells in the healing skin wound: Influential players at each stage of repair","volume":"58","author":"Wilgus","year":"2008","journal-title":"Pharmacol. Res."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1016\/j.smim.2014.01.005","article-title":"Transcriptional regulation of wound inflammation","volume":"26","author":"Haertel","year":"2014","journal-title":"Semin. Immunol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"3642","DOI":"10.4049\/jimmunol.176.6.3642","article-title":"Functional Characterization of the CCL25 Promoter in Small Intestinal Epithelial Cells Suggests a Regulatory Role for Caudal-Related Homeobox (Cdx) Transcription Factors","volume":"176","author":"Ericsson","year":"2006","journal-title":"J. Immunol."},{"key":"ref_44","unstructured":"Ericsson, A. (2005). Expression and regulation of CCL25 and its role in T cell localization and function within the small intestine. [Ph.D. Thesis, Faculty of Medicine, Lund University]."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"9415","DOI":"10.1073\/pnas.1300290110","article-title":"Macrophages are required for adult salamander limb regeneration","volume":"110","author":"Godwin","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"3946","DOI":"10.1111\/febs.16600","article-title":"CEMIP (HYBID, KIAA1199): Structure, function and expression in health and disease","volume":"290","author":"Spataro","year":"2023","journal-title":"FEBS J."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2021\/8475868","article-title":"PERK-Dependent Activation of the JAK2\/STAT3 Pathway Contributes to High Glucose-Induced Extracellular Matrix Deposition in Renal Tubular Epithelial Cells","volume":"2021","author":"Bao","year":"2021","journal-title":"Int. J. Endocrinol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"4225","DOI":"10.1242\/dev.125.21.4225","article-title":"Wnt-4 is a mesenchymal signal for epithelial transformation of metanephric mesenchyme in the developing kidney","volume":"125","author":"Kispert","year":"1998","journal-title":"Development"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1016\/S0092-8674(03)00432-X","article-title":"Mechanisms of TGF-\u03b2 Signaling from Cell Membrane to the Nucleus","volume":"113","author":"Shi","year":"2003","journal-title":"Cell"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"53","DOI":"10.18433\/J3K89D","article-title":"Hyaluronic Acid and Wound Healing","volume":"18","author":"Neuman","year":"2015","journal-title":"J. Pharm. Pharm. Sci."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1007\/s12015-007-0006-6","article-title":"Networking of WNT, FGF, Notch, BMP, and Hedgehog Signaling Pathways during Carcinogenesis","volume":"3","author":"Katoh","year":"2007","journal-title":"Stem Cell Rev."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1146\/annurev.cellbio.21.020604.150721","article-title":"RHO GTPASES: Biochemistry and Biology","volume":"21","author":"Jaffe","year":"2005","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1042\/BST0330891","article-title":"Rho GTPases and the control of cell behaviour","volume":"33","author":"Hall","year":"2005","journal-title":"Biochem. Soc. Trans."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1126\/science.1160809","article-title":"Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation","volume":"324","author":"Cantley","year":"2009","journal-title":"Science"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"14118","DOI":"10.1073\/pnas.1321349111","article-title":"Sequential switching of binding partners on PCNA during in vitro Okazaki fragment maturation","volume":"111","author":"Dovrat","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1093\/nar\/gkx1184","article-title":"Inhibition of DNA replication by an anti-PCNA aptamer\/PCNA complex","volume":"46","author":"Kowalska","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Lu, B. (2023). Evolutionary Insights into the Relationship of Frogs, Salamanders, and Caecilians and Their Adaptive Traits, with an Emphasis on Salamander Regeneration and Longevity. Animals, 13.","DOI":"10.3390\/ani13223449"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"22046","DOI":"10.3390\/ijms160922046","article-title":"Identification of Conserved and Novel MicroRNAs during Tail Regeneration in the Mexican Axolotl","volume":"16","author":"Gearhart","year":"2015","journal-title":"Int. J. Mol. Sci."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Holman, E.C., Campbell, L.J., Hines, J., and Crews, C.M. (2012). Microarray Analysis of microRNA Expression during Axolotl Limb Regeneration. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0041804"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"King, B.L., and Yin, V.P. (2016). A Conserved MicroRNA Regulatory Circuit Is Differentially Controlled during Limb\/Appendage Regeneration. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0157106"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"2257","DOI":"10.1073\/pnas.0510565103","article-title":"A microRNA expression signature of human solid tumors defines cancer gene targets","volume":"103","author":"Volinia","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"7065","DOI":"10.1158\/0008-5472.CAN-05-1783","article-title":"MicroRNA Gene Expression Deregulation in Human Breast Cancer","volume":"65","author":"Iorio","year":"2005","journal-title":"Cancer Res."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1053\/j.gastro.2007.05.022","article-title":"MicroRNA-21 Regulates Expression of the PTEN Tumor Suppressor Gene in Human Hepatocellular Cancer","volume":"133","author":"Meng","year":"2007","journal-title":"Gastroenterology"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1038\/ncb2037","article-title":"Genome-wide RNA-mediated interference screen identifies miR-19 targets in Notch-induced T-cell acute lymphoblastic leukaemia","volume":"12","author":"Mavrakis","year":"2010","journal-title":"Nat. Cell Biol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1016\/j.ccr.2006.04.020","article-title":"Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells","volume":"9","author":"Saito","year":"2006","journal-title":"Cancer Cell"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1158\/1940-6207.CAPR-11-0370","article-title":"Blood Cell Origin of Circulating MicroRNAs: A Cautionary Note for Cancer Biomarker Studies","volume":"5","author":"Pritchard","year":"2012","journal-title":"Cancer Prev. Res."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1111\/j.1365-2141.2008.07077.x","article-title":"Detection of elevated levels of tumour-associated microRNAs in serum of patients with diffuse large B-cell lymphoma","volume":"141","author":"Lawrie","year":"2008","journal-title":"Br. J. Haematol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Liu, M., Adelman, Z.N., and Zhang, L. (2014). TransPS: A Transcriptome Post Scaffolding Method for Assembling High Quality Contigs. Comput. Biol. J., 2014.","DOI":"10.1155\/2014\/961823"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.gene.2019.04.009","article-title":"Transcriptome analysis reveals novel insights in air-breathing magur catfish (Clarias magur) in response to high environmental ammonia","volume":"703","author":"Banerjee","year":"2019","journal-title":"Gene"},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. (2009). BLAST+: Architecture and applications. BMC Bioinf., 10.","DOI":"10.1186\/1471-2105-10-421"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"D140","DOI":"10.1093\/nar\/gkj112","article-title":"miRBase: microRNA sequences, targets and gene nomenclature","volume":"34","author":"Grocock","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10.","DOI":"10.1186\/gb-2009-10-3-r25"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1093\/nar\/gkr688","article-title":"miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades","volume":"40","author":"Mackowiak","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Love, M.I., Huber, W., and Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15.","DOI":"10.1186\/s13059-014-0550-8"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"Langfelder, P., and Horvath, S. (2008). WGCNA: An R package for weighted correlation network analysis. BMC Bioinform., 9.","DOI":"10.1186\/1471-2105-9-559"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: An R Package for Comparing Biological Themes Among Gene Clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS J. Integr. Biol."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"e133","DOI":"10.1093\/nar\/gku631","article-title":"The multiMiR R package and database: Integration of microRNA\u2013target interactions along with their disease and drug associations","volume":"42","author":"Ru","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: A software environment for integrated models of Biomolecular Interaction Networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"5","DOI":"10.6026\/97320630002005","article-title":"Mfuzz: A software package for soft clustering of microarray data","volume":"2","author":"Kumar","year":"2007","journal-title":"Bioinformation"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/25\/17\/9225\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T15:42:30Z","timestamp":1760110950000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/25\/17\/9225"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,8,25]]},"references-count":82,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2024,9]]}},"alternative-id":["ijms25179225"],"URL":"https:\/\/doi.org\/10.3390\/ijms25179225","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,8,25]]}}}